R/rare_multiplot.r

In rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

#' Combines rare_corrplot and rare_stacked into a single figure.
#' 
#' @inherit rare_corrplot
#' @inherit documentation_default
#' 
#' @family rarefaction
#' @family visualization
#' 
#' @export
#' @examples
#'     library(rbiom)
#'     
#'     rare_multiplot(hmp50, stat.by = "Body Site")
#'     

rare_multiplot <- function (
    biom, adiv = "Shannon", layers = "tc", rline = TRUE,
    stat.by = NULL, facet.by = NULL, colors = TRUE, shapes = TRUE, 
    test = "none", fit = "log", at = NULL, level = 0.95, p.adj = "fdr", 
    transform = "none", alt = "!=", mu = 0, caption = TRUE, check = FALSE, ... ) {
  
  
  #________________________________________________________
  # Build the two subplots, then arrange them together.
  #________________________________________________________
  corrplot <- rare_corrplot(
    biom      = biom, 
    adiv      = adiv, 
    layers    = layers, 
    rline     = rline, 
    stat.by   = stat.by, 
    facet.by  = facet.by, 
    colors    = colors, 
    shapes    = shapes, 
    test      = test, 
    fit       = fit, 
    at        = at, 
    level     = level, 
    p.adj     = p.adj, 
    transform = transform, 
    alt       = alt, 
    mu        = mu, 
    caption   = caption, 
    check     = check, 
    ...  )
  
  stacked <- rare_stacked(
    biom  = biom, 
    rline = rline )
  
  plots <- list(corrplot = corrplot, stacked = stacked)
  
  
  p <- patchwork::wrap_plots(plots, ncol = 1) %>% 
    add_class('rbiom_plot')
  
  attr(p, 'stats') <- attr(corrplot, 'stats', exact = TRUE)
  attr(p, 'data')  <- lapply(plots, attr, which = 'data', exact = TRUE)
  
  attr(p, 'code') <- paste(collapse = "\n\n", local({
    
    cmds <- sapply(seq_along(plots), function (i) {
      sub(
        x           = attr(plots[[i]], 'code'), 
        pattern     = "ggplot(data", 
        replacement = sprintf("p%i <- ggplot(data[[%s]]", i, single_quote(names(plots)[[i]])),
        fixed       = TRUE )
    })
    c(cmds, sprintf("patchwork::wrap_plots(%s, ncol = 1)", paste0(collapse = ", ", "p", seq_along(plots))))
    
  })) %>% add_class('rbiom_code')
  
  
  
  attr(p, 'cmd') <-  current_cmd('rare_multiplot')
  
  return (p)
}